OLIN (version 1.50.0)

fdr.spatial2: Assessment of the significance of spatial bias

Description

This function assesses the significance of spatial bias by a one-sided random permutation test. This is achieved by comparing the observed average values of logged fold-changes within a spot's spatial neighbourhood with an empirical distribution generated by random permutation. The significance of spatial bias is given by the false discovery rate.

Usage

fdr.spatial2(object,delta=2,N=100,av="median",edgeNA=FALSE)

Arguments

object

object of class marrayRaw or marrayNorm

delta

integer determining the size of spot neighbourhoods ((2*delta+1)x(2*delta+1)).

N

number of random permutations performed for generation of empirical background distribution

av

averaging of M within neighbourhood by mean or median (default)

edgeNA

treatment of edges of array: For edgeNA=TRUE, the significance of a neighbourhood (defined by a sliding window) is set to NA, if the neighbourhood extends over the edges of the matrix.

Value

FDRp) and negative (FDRn) deviations of $median/mean of \code{M}$ of the spot's neighbourhood is produced. Each vector contains the false discovery values for one array.

Details

The function fdr.spatial2.Rd is basically the same as fdr.spatial, but differs in its input and output formats. Details about the functionality can be found at fdr.spatial.

See Also

p.spatial, fdr.int, sigxy.plot,

Examples

# To run these examples, delete the comment signs before the commands.
#
# LOADING DATA
# data(sw)
#
# CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS
# For this illustration, N was chosen rather small. For "real" analysis, it should be larger.
# FDR <- fdr.spatial2(sw,delta=2,N=10,av="median",edgeNA=TRUE)
#
# SIGNIFICANCE PLOTS OF ARRAY 1
# sigxy.plot2(sw[,1],FDR$FDRp[[1]],FDR$FDRn[[1]],color.lim=c(-5,5),main="FDR")
# SIGNIFICANCE PLOTS OF ARRAY 3
# sigxy.plot2(sw[,3],FDR$FDRp[[3]],FDR$FDRn[[3]],color.lim=c(-5,5),main="FDR")
#